2020(S11) Lecture:week 3

Week 3 Tuesday

coliRoids

Bacteria as pixels

BioPrimer6: Picture this!

E. coli do not normally respond to light but a recent publication describes a combination of genes that lead to light-responsive expression of β-galactosidase in E. coli. Recall from your study of the lac operon in biology classes that β-galactosidase is an enzyme encoded by the LacZ gene. Normally the protein cleaves the disaccharide, lactose, into two monosaccharides, galactose and glucose.

For the bacterial photography system, the "coliroid" cells producing LacZ cleave an indicator compound, giving rise to a black precipitate. When the cells are grown in the dark, transcription of LacZ is high and the indicator in the media turns black. When the cells are grown in the light, there is very little transcription of the LacZ gene and the media’s natural color (yellowish) shows through.

For today, you can get used to this system. You’ll plate a layer of cells on indicator medium, and then incubate the dish with a mask until next time. You and a partner can pick any image you'd like to develop. You expect the dark-grown plate to turn a dark color and the light-grown plate to stay light.

Why are we doing this?? The bacterial photography system was one of the very first successes from the iGEM summer competition. It provides an instance proof that a small group of motivated undergraduates and some clever advisers can engineering biology to do their bidding. The project also highlights how an understanding of basic biology (e.g. the lac operon and two component signaling) can lead to new applications when refined and improved.

Week 3 Studio

Abstraction

In designing a synthetic biological system it can be helpful (to you and to others) to describe the system using a high level design language that can simplify or "abstract" what's going on with the system. For example the bacterial photography system might be depicted as two key devices, one device that detects a signal and a second device that generates an output upon receiving information from the first device. Such a “black box” depiction of the system's operation enables easy re-use of the devices by others as well as helpful specifications for the needed connections between the devices (versus the materials needed for operation within them). For example, light is the input for the bacterial photography system, but it's straightforward to retask the system as a chemical sensor instead: just swap out the first "input sensing device" from one that's sensitive to light to one that's sensitive to your chemical of interest. Similarly, the output of the bacterial photography system is a black colored product but imagine hooking up the light sensing input device to chemotaxis as the output...then the cells might swim to the light rather than turn a color in response.

"Black box" depiction of bacterial photography system

Homework

Week 3 Thursday

Getting to 3 ideas

We will not meet as a class today but you are expected to spend the 1.5 hours that you might have enjoyed in 26-152 looking at the requirements for the upcoming 3-Ideas Presentations and planning a project for which you can articulate at least 3 of these 5 points:

1. What: what problem or opportunity are you thinking of focusing on? How sweeping or focused is this idea?
2. How: what approach could you take to make a dent in the problem?
3. What if if your project is fully successful, how big a difference could it make? what concerns does it raise?
4. What else are there other technologies that can be used/have been used to address this area?
5. Dunno how big are the gaps in what you know? how much is completely unknown or unknowable?

Homework Email your thoughts and your response to these questions to nkuldell AT mit DOT edu no later than Tuesday 2.22.11 at 2:22PM. The information will be used to group you into discussion groups for Wednesday's studio.